Bump stops are there to save the spring from bending negative. You set the bump stops so that they stop the spring when it goes flat. I too have YJs on my samurai. They are just stock height springs, 4 pack front, 5 pack rear. I have about 3 to 3.5" up travel.
A track bar is a good thing to have when using leaf springs, definitely want to cut down on wheel hop. I would say go with one again. I still suffer from hopping when i get on the throttle.
You can run Toyota CV drive shafts front and rear. The best year(s) to get are the 84-85 front drive shaft, they have a 35 degree max operating angle. The 85+ are only 25 degree or less operating angle. But you can modify them to operate at 35 degrees.
Here's a link to a pretty good write up on had to do this.
http://www.4x4wire.com/toyota/tech/cvmod/This is what I did to my front drive shaft, so far so good. I do have a pretty nasty front pinion angle so the drive shaft does bind at full droop.
Another option for the front is an 89-94 V6 4Runner rear drive shaft, its a non CV drive shaft with a 42 degree operation angle. I am thinking about going with this option, or at least try it out.
Hope that helps
Amilla